## Loading required package: ggplot2
## Loading required package: cowplot
## 
## ********************************************************
## Note: As of version 1.0.0, cowplot does not change the
##   default ggplot2 theme anymore. To recover the previous
##   behavior, execute:
##   theme_set(theme_cowplot())
## ********************************************************
## Loading required package: Matrix
## Registered S3 method overwritten by 'R.oo':
##   method        from       
##   throw.default R.methodsS3
## 
## Attaching package: 'tidyr'
## The following objects are masked from 'package:Matrix':
## 
##     expand, pack, unpack
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
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##     intersect, setdiff, setequal, union
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## Attaching package: 'magrittr'
## The following object is masked from 'package:tidyr':
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##     extract

Look at changes in gene expression of lola target genes

Project: Promoter Opening

Author: Vivek

Generated: Mon Jan 24 2022, 06:15 AM

## Scaling data matrix
## Scaling data matrix
## Scaling data matrix

## Scaling data matrix
## Scaling data matrix
## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in dtw(x = align.1, y = align.2, keep.internals = TRUE, dist.method
## = metric.use): Argument dist.method does not usually make a difference with
## single-variate timeseries

## Warning in as_grob.default(plot): Cannot convert object of class environment
## into a grob.

## Warning in as_grob.default(plot): Cannot convert object of class NULL into a
## grob.

Session information

For reproducibility, this analysis was performed with the following R/Bioconductor session:

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RColorBrewer_1.1-2 magrittr_1.5       dplyr_0.8.3        tidyr_1.0.0       
[5] Seurat_2.3.1       Matrix_1.2-17      cowplot_1.0.0      ggplot2_3.2.1     
[9] pander_0.6.3      

loaded via a namespace (and not attached):
  [1] diffusionMap_1.2.0   Rtsne_0.15           VGAM_1.1-3          
  [4] colorspace_1.4-1     ellipsis_0.2.0.1     ggridges_0.5.1      
  [7] class_7.3-15         modeltools_0.2-23    mclust_5.4.6        
 [10] htmlTable_1.13.1     base64enc_0.1-3      proxy_0.4-24        
 [13] rstudioapi_0.10      npsurv_0.4-0         flexmix_2.3-17      
 [16] prodlim_2019.11.13   lubridate_1.7.9      ranger_0.12.1       
 [19] codetools_0.2-16     splines_3.6.1        R.methodsS3_1.7.1   
 [22] lsei_1.2-0           robustbase_0.93-6    knitr_1.24          
 [25] zeallot_0.1.0        tclust_1.4-2         jsonlite_1.6        
 [28] Formula_1.2-3        Cairo_1.5-10         pROC_1.16.2         
 [31] caret_6.0-86         ica_1.0-2            cluster_2.1.0       
 [34] kernlab_0.9-29       png_0.1-7            R.oo_1.22.0         
 [37] compiler_3.6.1       backports_1.1.4      assertthat_0.2.1    
 [40] lazyeval_0.2.2       lars_1.2             acepack_1.4.1       
 [43] htmltools_0.3.6      tools_3.6.1          igraph_1.2.4.1      
 [46] gtable_0.3.0         glue_1.3.1           RANN_2.6.1          
 [49] reshape2_1.4.3       Rcpp_1.0.5           jquerylib_0.1.4     
 [52] vctrs_0.2.0          gdata_2.18.0         ape_5.3             
 [55] nlme_3.1-141         iterators_1.0.12     fpc_2.2-8           
 [58] lmtest_0.9-37        gbRd_0.4-11          timeDate_3043.102   
 [61] xfun_0.29            gower_0.2.2          stringr_1.4.0       
 [64] lifecycle_0.1.0      irlba_2.3.3          gtools_3.8.1        
 [67] DEoptimR_1.0-8       zoo_1.8-6            MASS_7.3-51.4       
 [70] scales_1.0.0         ipred_0.9-9          doSNOW_1.0.18       
 [73] parallel_3.6.1       reticulate_1.13      pbapply_1.4-2       
 [76] gridExtra_2.3        segmented_1.2-0      rpart_4.1-15        
 [79] latticeExtra_0.6-28  stringi_1.4.3        foreach_1.5.0       
 [82] checkmate_1.9.4      caTools_1.17.1.2     bibtex_0.4.2        
 [85] lava_1.6.8           dtw_1.22-3           Rdpack_0.11-0       
 [88] SDMTools_1.1-221.1   rlang_0.4.0          pkgconfig_2.0.2     
 [91] prabclus_2.3-2       bitops_1.0-6         evaluate_0.14       
 [94] lattice_0.20-38      ROCR_1.0-7           purrr_0.3.2         
 [97] labeling_0.3         recipes_0.1.13       htmlwidgets_1.3     
[100] tidyselect_0.2.5     plyr_1.8.4           R6_2.4.0            
[103] snow_0.4-3           gplots_3.0.1.1       generics_0.0.2      
[106] Hmisc_4.2-0          pillar_1.4.2         foreign_0.8-72      
[109] withr_2.1.2          mixtools_1.2.0       fitdistrplus_1.0-14 
[112] survival_2.44-1.1    scatterplot3d_0.3-41 nnet_7.3-12         
[115] tsne_0.1-3           tibble_2.1.3         crayon_1.3.4        
[118] KernSmooth_2.23-15   rmarkdown_2.11       grid_3.6.1          
[121] data.table_1.12.2    FNN_1.1.3            ModelMetrics_1.2.2.2
[124] metap_1.1            digest_0.6.20        diptest_0.75-7      
[127] R.utils_2.9.0        stats4_3.6.1         munsell_0.5.0